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CBNplot

plot bayesian network inferred from gene expression data based on enrichment analysis results


Bioconductor version: Release (3.18)

This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

Author: Noriaki Sato [cre, aut]

Maintainer: Noriaki Sato <nori at hgc.jp>

Citation (from within R, enter citation("CBNplot")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CBNplot")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CBNplot")
CBNplot HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, NetworkInference, Pathways, Reactome, Software, Visualization
Version 1.2.1
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang, oaqc
System Requirements
URL https://github.com/noriakis/CBNplot
Bug Reports https://github.com/noriakis/CBNplot/issues
See More
Suggests knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CBNplot_1.2.1.tar.gz
Windows Binary CBNplot_1.2.1.zip
macOS Binary (x86_64) CBNplot_1.2.1.tgz
macOS Binary (arm64) CBNplot_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/CBNplot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CBNplot
Bioc Package Browser https://code.bioconductor.org/browse/CBNplot/
Package Short Url https://bioconductor.org/packages/CBNplot/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive